Phenotype and GWAS Information:

Agronomic Traits

Note: All the agronomic trait is from the article Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection.

Metabolic Traits

Note: All the metabolic trait is from the article Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism. Some metabolics have two replications, the second replication is end with '_2', like 'mr1002_2'.

Search Results:

The detailed information about mr1177 can be find at here.

GWAS Results:

Note: If the P-value of Linear Regression (LR) or Linear Mixed Model (LMM) ≤ 1e-5 or the rank ≤ 20000, the results are saved. Only the LMM results are plotted below.

Significant Candidate Loci (Lead SNP):

Variation IDVariation ID V6ChromosomePositionLR P-value LMM P-value
vg0202256731 sf0202256730 2 2256731 6.93E-11 5.29E-06
vg0104046268 sf0104045268 1 4046268 3.15E-10 4.57E-07
vg0918977054 sf0918976054 9 18977054 5.39E-09 NA
vg0804833917 sf0804832920 8 4833917 7.36E-09 2.97E-06
vg1007617621 sf1007633230 10 7617621 9.00E-09 NA
vg0805568634 sf0805567637 8 5568634 2.29E-08 5.04E-07
vg1107588911 sf1107584656 11 7588911 2.29E-07 6.60E-07
vg1207676050 sf1207673454 12 7676050 2.84E-07 2.39E-06
vg0422210905 sf0422025786 4 22210905 3.53E-07 NA
vg1000986102 sf1000985078 10 986102 1.40E-06 1.03E-06
vg1005434645 sf1005451182 10 5434645 1.44E-06 3.58E-06
vg0714075702 sf0714074709 7 14075702 7.00E-06 NA